Water-bridged hydrogen bond formation between 5-hydroxylmethylcytosine (5-hmC) and its 3'-neighbouring bases in A- and B-form DNA duplexes

Rui Wang; Srivathsan V Ranganathan; Vibhav A Valsangkar; Stephanie M Magliocco; Fusheng Shen; Alan Chen; Jia Sheng

doi:10.1039/c5cc06563a

Water-bridged hydrogen bond formation between 5-hydroxylmethylcytosine (5-hmC) and its 3'-neighbouring bases in A- and B-form DNA duplexes

Chem Commun (Camb). 2015 Nov 25;51(91):16389-92. doi: 10.1039/c5cc06563a.

Authors

Rui Wang¹, Srivathsan V Ranganathan¹, Vibhav A Valsangkar¹, Stephanie M Magliocco¹, Fusheng Shen¹, Alan Chen¹, Jia Sheng¹

Affiliation

¹ Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA. [email protected].

PMID: 26411524
DOI: 10.1039/c5cc06563a

Abstract

5-Hydroxylmethylcytosine (5hmC) has been recognized as the sixth base with important biological functions in many tissues and cell types. We present here the high-resolution crystal structures and molecular simulation studies of both A-form and B-form DNA duplexes containing 5hmC. We observed that 5hmC interacts with its 3'-neighboring bases through water-bridged hydrogen bonds and these interactions may affect the further oxidation of 5hmC.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

5-Methylcytosine / analogs & derivatives
Base Pairing
Crystallography, X-Ray
Cytosine / analogs & derivatives*
Cytosine / chemistry
DNA, A-Form / chemistry*
DNA, A-Form / ultrastructure
DNA, B-Form / chemistry*
DNA, B-Form / ultrastructure
Hydrogen Bonding*
Molecular Dynamics Simulation
Water / chemistry*

Substances

DNA, A-Form
DNA, B-Form
Water
5-hydroxymethylcytosine
5-Methylcytosine
Cytosine